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protocols::rna::AlignmentEnergy Class Reference

An RMSD-type energy to a reference pose, complete with derivatives hacked out of coordinate constraints. More...

#include <AlignmentEnergy.hh>

Inheritance diagram for protocols::rna::AlignmentEnergy:
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Public Member Functions

 AlignmentEnergy (core::scoring::methods::EnergyMethodOptions const &options)
 
 ~AlignmentEnergy () override
 
core::scoring::methods::EnergyMethodOP clone () const override
 Clone: create a copy of this object, and return an owning pointer to the copy. More...
 
void setup_for_scoring (core::pose::Pose &pose, core::scoring::ScoreFunction const &) const override
 Indicate required setup steps for scoring. More...
 
void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override
 Is the score context dependent or context independent? More...
 
core::Size version () const override
 Indicates the current version of this score term. More...
 
void finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) const override
 Actually calculate the total energy. More...
 
void eval_atom_derivative (core::id::AtomID const &id, core::pose::Pose const &pose, core::kinematics::DomainMap const &domain_map, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap const &emap, core::Vector &F1, core::Vector &F2) const override
 
void align_pose (core::pose::PoseOP const &align_pose)
 
protocols::stepwise::modeler::align::StepWisePoseAlignerOP
const & 
pose_aligner () const
 
void rmsd_screen (core::Real const setting)
 
- Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
 WholeStructureEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...
 
 ~WholeStructureEnergy () override
 
EnergyMethodType method_type () const override
 Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...
 
virtual Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy? More...
 
- Public Member Functions inherited from core::scoring::methods::EnergyMethod
 EnergyMethod (EnergyMethodCreatorOP creator)
 Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...
 
virtual void setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
 if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...
 
virtual void prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
 If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...
 
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...
 
virtual void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
 Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...
 
virtual void setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
 Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...
 
virtual void finalize_after_minimizing (pose::Pose &pose) const
 Called after minimization, allowing a derived class to do some teardown steps. More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
 called at the end of derivatives evaluation More...
 
virtual bool minimize_in_whole_structure_context (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...
 
virtual bool defines_high_order_terms (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
 Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...
 
ScoreTypes const & score_types () const
 Returns the score types that this energy method computes. More...
 
virtual void show_additional_info (std::ostream &, pose::Pose &, bool) const
 show additional information of the energy method More...
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Private Types

typedef
core::scoring::methods::WholeStructureEnergy 
parent
 

Private Attributes

core::pose::PoseOP align_pose_
 
utility::vector1< core::Sizemoving_res_list_
 
core::scoring::func::FuncOP func_
 
protocols::stepwise::modeler::align::StepWisePoseAlignerOP pose_aligner_
 
core::Real rmsd_screen_
 

Additional Inherited Members

- Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod parent
 
- Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase parent
 
- Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void set_score_types (EnergyMethodCreatorOP creator)
 Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...
 

Detailed Description

An RMSD-type energy to a reference pose, complete with derivatives hacked out of coordinate constraints.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::rna::AlignmentEnergy::AlignmentEnergy ( core::scoring::methods::EnergyMethodOptions const &  options)
protocols::rna::AlignmentEnergy::~AlignmentEnergy ( )
inlineoverride

Member Function Documentation

void protocols::rna::AlignmentEnergy::align_pose ( core::pose::PoseOP const &  align_pose)

References align_pose_, and pose_aligner_.

core::scoring::methods::EnergyMethodOP protocols::rna::AlignmentEnergy::clone ( ) const
overridevirtual

Clone: create a copy of this object, and return an owning pointer to the copy.

Implements core::scoring::methods::EnergyMethod.

void protocols::rna::AlignmentEnergy::eval_atom_derivative ( core::id::AtomID const &  id,
core::pose::Pose const &  pose,
core::kinematics::DomainMap const &  domain_map,
core::scoring::ScoreFunction const &  sfxn,
core::scoring::EnergyMap const &  emap,
core::Vector F1,
core::Vector F2 
) const
override
void protocols::rna::AlignmentEnergy::finalize_total_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  ,
core::scoring::EnergyMap totals 
) const
overridevirtual
void protocols::rna::AlignmentEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
overridevirtual

Is the score context dependent or context independent?

Implements core::scoring::methods::EnergyMethod.

protocols::stepwise::modeler::align::StepWisePoseAlignerOP const& protocols::rna::AlignmentEnergy::pose_aligner ( ) const
inline

References pose_aligner_.

void protocols::rna::AlignmentEnergy::rmsd_screen ( core::Real const  setting)

References func_, and rmsd_screen_.

void protocols::rna::AlignmentEnergy::setup_for_scoring ( core::pose::Pose pose,
core::scoring::ScoreFunction const &   
) const
overridevirtual

Indicate required setup steps for scoring.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::update_residue_neighbors().

core::Size protocols::rna::AlignmentEnergy::version ( ) const
overridevirtual

Indicates the current version of this score term.

Implements core::scoring::methods::EnergyMethod.

Member Data Documentation

core::pose::PoseOP protocols::rna::AlignmentEnergy::align_pose_
private
core::scoring::func::FuncOP protocols::rna::AlignmentEnergy::func_
private
utility::vector1< core::Size > protocols::rna::AlignmentEnergy::moving_res_list_
private
protocols::stepwise::modeler::align::StepWisePoseAlignerOP protocols::rna::AlignmentEnergy::pose_aligner_
private
core::Real protocols::rna::AlignmentEnergy::rmsd_screen_
private

Referenced by AlignmentEnergy(), and rmsd_screen().


The documentation for this class was generated from the following files: